Several years after the original film, Phoebus and Esmeralda have married and have a son named Zephyr. Quasimodo is now free to interact with the public; however, he continues to live in the cathedral with his gargoyle friends Victor, Hugo, and Laverne.
A circus of thieves, led by Sarousch, enters town to steal Notre Dame's most beloved bell: La Fidèle, the inside of which is decorated with enormous jewels of various colors. He sends Madellaine, his beautiful assistant, to discover the whereabouts of La Fidèle; however, she runs away after seeing Quasimodo. The gargoyles convince Quasimodo to go to the circus in an attempt to court Madellaine. Sarousch wows the audience when he makes an elephant disappear while his associates steal from the audience. Sarousch forces Madellaine to follow Quasimodo and obtain the information he wants. She follows Quasimodo and Zephyr, and after seeing how gentle Quasimodo is with Zephyr, his appearance no longer bothers her. Quasimodo takes her around Paris, and shows her numerous sights.
Meanwhile, Phoebus receives reports of robberies and sets out on his horse, Achilles, to investigate. The gargoyles and a group of people sing a song that tells about how Quasimodo and Madellaine are in love just as rain begins to fall and Quasimodo and Madellaine run into the cathedral. Madellaine dries off behind a curtain, and Quasimodo shows her La Fidèle. Quasimodo gives Madellaine a figurine he made of her, and he tells her that she can now see herself through his eyes. Tears well up in Madellaine's eyes, and after kissing Quasimodo on the forehead, she leaves.
The next day, Quasimodo feels odd; one minute he feels sick, the next he feels energetic. After he seeks Esmeralda's help, she realizes he is in love with Madellaine and tells him he must tell Madellaine of his feelings. Phoebus enters and declares that the circus is responsible for a string of thefts in which Madellaine might be implicated, which do not delight the other main characters (Quasimodo due to being in love with Madellaine, Esmeralda due to believing that Phoebus still holds prejudice views towards gypsies, and Zephyr due to admiring the circus).
Sarousch convinces Madellaine to distract Quasimodo while he steals La Fidèle, and she reluctantly agrees. Later, while Quasimodo is out with Madellaine, Sarousch and two of his subordinates sneak into the cathedral. Zephyr and Djali the goat follow them and watch as Sarousch causes La Fidèle to vanish. The gargoyles, who had tried to drop a bell on the thieves, end up trapped under it; Laverne rams one of its sides, causing the bell to clang loudly. Hearing the sound, Quasimodo and Madellaine rush back. When it is discovered that La Fidèle has been stolen, Clopin says if they don't find the bell, the festival will be ruined. Phoebus guesses that Sarousch is responsible. He sends the soldiers all over Paris to find Sarousch. Quasimodo assumes that Madellaine has used him, and tells Phoebus that he was right and he runs back into the cathedral. Pheobus apologizes to Quasimodo and has Madellaine arrested, and after realizing that he lost his true love and can no longer trust her, Quasimodo starts crying on the steps of Notre Dame feeling miserable, used and betrayed.
Quasimodo climbs to the bell tower, hears the gargoyles calling, and pulls the bell off them. After they tell him Zephyr left to pursue Sarousch, Quasimodo and Esmeralda rush to the Palace of Justice to tell Phoebus. Madellaine, who is locked in a cell, tells them Sarousch has taken the bell underground. Although Esmeralda convinces her husband to trust Madellaine's word, he nevertheless binds Madellaine's hands and forces her to accompany him.
Quasimodo and the others venture into the dank catacombs. They encounter Djali, who takes them to Sarousch and Zephyr. Sarousch forces Phoebus into opening the gate to allow his raft through by using Zephyr as a hostage. Madellaine convinces Quasimodo to trust her, and the pair run up a stairwell. Quasimodo lassoes a rock to create a tightrope, and Madellaine walks across it. When the raft passes beneath her, Madellaine seizes Zephyr from Sarousch's grasp. Sarousch is arrested, and the film ends with Quasimodo and Madellaine proclaiming their love for each other while Zephyr rings La Fidèle.